Locus 4011

Sequence ID 3L_DroMel_CAF1
Location 11,712,137 – 11,712,256
Length 119
Max. P 0.997087
window6248 window6249

overview

Window 8

Location 11,712,137 – 11,712,256
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 92.86
Mean single sequence MFE -39.88
Consensus MFE -35.24
Energy contribution -35.80
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.46
Structure conservation index 0.88
SVM decision value 0.99
SVM RNA-class probability 0.895962
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11712137 119 + 23771897
UGGGAUCCAGGCAGCAGGAGCAGUAGCAUGAUUCAGAGCAGCAAACCCGCUUAAACUGCGGGCCACGUAUUGAUGUGCUCUGAUUCUGUGGUUAAUUUCCCAUCCGCAGAUGUACCUGC
(((((....(((.((((((((....)).....(((((((......(((((.......)))))..((((....))))))))))))))))).)))....)))))...((((......)))) ( -42.60)
>DroSec_CAF1 25364 119 + 1
UGGCAUCCAGGCAGCAGGAGCAGGAGCAGGAUUCAGAGCAGCAAACCCGCUUAAACUGCGGGCCACGUAUUGAUGUGCUCUGAUUCUGUGGUUAAUUUCCCAUCAGCAGAUGUACCUGC
..((......)).(((((.(((...((.(((.(((((((......(((((.......)))))..((((....))))))))))).)))((((........))))..))...))).))))) ( -42.10)
>DroSim_CAF1 21320 113 + 1
UGGCAUCCAGGCAGCAGG------AGCAUGAUUCAGAACAGCAAACCCGCUUAAACUGCGGGCCACGUAUUGAUGUGCUCUGAUUCUGUGGUUAAUUUCCCAUCAGCAGAUGUACCUGC
..((......)).(((((------.((((((.(((((........(((((.......))))).(((((....))))).))))).)).((((........))))......)))).))))) ( -34.20)
>DroEre_CAF1 21412 119 + 1
UGGCAGCCAGGCAGCAGGAGCAGGUGCAGCAUUCAGAGCAGCAAACCCGCUUUAACUGCGGGCCACGUAUUGAUGUGCUCUGAUUCUGUGGUUAAUUUCCCAUCAGCAUAUGUGCCUGU
..((......)).(((((.(((.((((.....(((((((......(((((.......)))))..((((....)))))))))))....((((........))))..)))).))).))))) ( -40.70)
>DroYak_CAF1 21376 119 + 1
UGGCAUCCAGGCAGUAGGCACAGGAGCAGGAUUCAGAGCAGCAAACCCGCUUAAACUGCGGGCCACGUAUUGAUGUGCUCUGAUUCUGUGGUUAAUUUCCCAUCAGCAUAUGUACCUGC
..((......)).(((((.(((...((.(((.(((((((......(((((.......)))))..((((....))))))))))).)))((((........))))..))...))).))))) ( -39.80)
>consensus
UGGCAUCCAGGCAGCAGGAGCAGGAGCAGGAUUCAGAGCAGCAAACCCGCUUAAACUGCGGGCCACGUAUUGAUGUGCUCUGAUUCUGUGGUUAAUUUCCCAUCAGCAGAUGUACCUGC
.............(((((.(((...((..((.(((((((......(((((.......)))))..((((....))))))))))).)).((((........))))..))...))).))))) (-35.24 = -35.80 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,712,137 – 11,712,256
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 92.86
Mean single sequence MFE -40.94
Consensus MFE -36.56
Energy contribution -36.44
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.06
Structure conservation index 0.89
SVM decision value 2.80
SVM RNA-class probability 0.997087
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11712137 119 - 23771897
GCAGGUACAUCUGCGGAUGGGAAAUUAACCACAGAAUCAGAGCACAUCAAUACGUGGCCCGCAGUUUAAGCGGGUUUGCUGCUCUGAAUCAUGCUACUGCUCCUGCUGCCUGGAUCCCA
.((((((((...((((.(((........)))..((.(((((((((((......)))((((((.......))))))....)))))))).))......))))...)).))))))....... ( -42.60)
>DroSec_CAF1 25364 119 - 1
GCAGGUACAUCUGCUGAUGGGAAAUUAACCACAGAAUCAGAGCACAUCAAUACGUGGCCCGCAGUUUAAGCGGGUUUGCUGCUCUGAAUCCUGCUCCUGCUCCUGCUGCCUGGAUGCCA
(((((........(((.(((........))))))..(((((((((((......)))((((((.......))))))....))))))))..)))))....(((((........))).)).. ( -42.10)
>DroSim_CAF1 21320 113 - 1
GCAGGUACAUCUGCUGAUGGGAAAUUAACCACAGAAUCAGAGCACAUCAAUACGUGGCCCGCAGUUUAAGCGGGUUUGCUGUUCUGAAUCAUGCU------CCUGCUGCCUGGAUGCCA
(((((..(((...(((.(((........))))))..(((((((((((......)))((((((.......))))))....))))))))...)))..------)))))............. ( -37.30)
>DroEre_CAF1 21412 119 - 1
ACAGGCACAUAUGCUGAUGGGAAAUUAACCACAGAAUCAGAGCACAUCAAUACGUGGCCCGCAGUUAAAGCGGGUUUGCUGCUCUGAAUGCUGCACCUGCUCCUGCUGCCUGGCUGCCA
.((((((((...((...(((........)))(((..(((((((((((......)))((((((.......))))))....))))))))...))).....))...)).))))))....... ( -41.60)
>DroYak_CAF1 21376 119 - 1
GCAGGUACAUAUGCUGAUGGGAAAUUAACCACAGAAUCAGAGCACAUCAAUACGUGGCCCGCAGUUUAAGCGGGUUUGCUGCUCUGAAUCCUGCUCCUGUGCCUACUGCCUGGAUGCCA
(((((........(((.(((........))))))..(((((((((((......)))((((((.......))))))....))))))))..)))))(((.(.((.....))).)))..... ( -41.10)
>consensus
GCAGGUACAUCUGCUGAUGGGAAAUUAACCACAGAAUCAGAGCACAUCAAUACGUGGCCCGCAGUUUAAGCGGGUUUGCUGCUCUGAAUCCUGCUCCUGCUCCUGCUGCCUGGAUGCCA
.((((((......(((.(((........))))))..(((((((((((......)))((((((.......))))))....))))))))...................))))))....... (-36.56 = -36.44 +  -0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:22 2006